Clifford’s
http://www.clifford.com/ G4 and G5 AvantGuard series alarms can control everything you are looking for using a serial connection. Not sure if that is what you are wanting or not wanting when you say you can't use external modules.
To answer your original question, my experience is limited to Fords, but using there hand held diagnostic scanner (NGS) you can control many of the types of things you are wanting (things controlled by the BCM and some things controlled by the PCM). This isn't using OBD protocol, but does use the same port.